<smacking you on the nose with a rolled up newspaper - bad kowilato> 
There is an ongoing issue where it looks like buyers are being charged FedEx retail prices at checkout when the pricing should be the discounted prices. eBay has "top men" on it as we speak. "top men".
That doesn't involve dimensional weights, oversize, or anything else of the sort - just what appears to be a case of the calculator using the wrong lookup table at checkout (in other words, the inflated prices presented to buyers are the correct pricing for the pkgs at counter rates in the few cases I've seen)
If you want to dissect the shipment from your OP that had the problem to see if the numbers and planets align with the theory:
Actual package Weight
Actual accurate package Dimensions
Origin zip code
Destination zip code
Destination commercial or residential?
Date of the shipment? (to select correct fuel surcharge)
Service used (Ground/Home Delivery/SmartPost)
Amounts of any other addons like Signature Reqd, insurance, handling fee, etc
Anything non-standard about the package? Not boxed, is a long cylinder, in a crate, etc.
Dropped off at FedEx location or scheduled pickup?
What was estimated shipping amount at label creation time?
What was the exact charge and the charged weight and dimensions on the eBay invoice?
Were there additional charges on the eBay invoice? If so, what and how much?
How much exactly was the buyer charged?
